VMD-L Mailing List

From: Michael Patzschke (patzsc21_at_hzdr.de)
Date: Sat Apr 11 2015 - 07:52:35 CDT

Hi,

I can confirm, that this solves my problems. Thank you very much
for your help!

Regards,
Michael

> On 10 Apr 2015, at 22:06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> In case you didn't see my other posting last night,
> I recently exchanged many emails with Adrian Roitberg who had
> the same Mac problem, and it seems that we have found a short-term
> workaround for the MacOS X Yosemite 10.10.2 update problems that
> have recently cropped up on certain varieties of Mac laptops.
> The solution is to set an environment variable to tell VMD not to
> use the MacOS-provided file browser window, and to instead use the
> FLTK-based file chooser. This is done by setting the environment variable
> "VMDFILECHOOSER" to the value "FLTK". This can be done in VMD itself
> in the text console, in the user's .vmdrc file, in the global .vmdrc
> file in the VMD.app bundle, or by setting the environment variable in the
> user's Unix shell .bashrc, etc.
>
> To set the variable in VMD or .vmdrc etc, run this command:
> set env(VMDFILECHOOSER) FLTK
>
> To set the variable in bash, add this to .bashrc etc:
> VMDFILECHOOSER=FLTK
> export VMDFILECHOOSER
>
> After the environment variable is set, VMD will use the alternative
> file selector window in the graphical interface, and this should prevent
> the problems you've been encountering.
>
> Let me know if the workaround is successful for you.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Sat, Feb 14, 2015 at 04:02:28AM +0100, Michael Patzschke wrote:
>> John,
>> Thank you very much for your efforts! I have to apologise, when I first
>> started this thread I had limited internet access. Now I have searched
>> a bit more and it seems that man yosemite users experience this problem.
>> There is actually a solution, although one that implies, that the problem
>> might not be OpenGL related. The problem appears always and only if
>> one uses the â**Browseâ** button in the Molecule File Browser. If one
>> gives
>> the name of a pdb file (download from [1]pdb.org) or the complete path of
>> the local file one wants to open everything is fine. it is also no problem
>> to
>> start vmd directly with a filename.
>> Also to answer your question on the os version:
>> System Version: OS X 10.10.2 (14C109)
>> Kernel Version: Darwin 14.1.0
>> And the machine:
>> Model Identifier: MacBookPro11,3
>> Processor Name: Intel Core i7
>> Processor Speed: 2,5 GHz
>> Number of Processors: 1
>> Total Number of Cores: 4
>> L2 Cache (per Core): 256 KB
>> L3 Cache: 6 MB
>> Memory: 16 GB
>> Thanks again,
>> Michael
>>
>> On 13 Feb 2015, at 18:26, John Stone <[2]johns_at_ks.uiuc.edu> wrote:
>> Michael,
>> On the new machine, what specific Yosemite version number are you
>> running?
>> This sounds to me like a Yosemite issue (again) rather than a VMD issue,
>> but having more system details is helpful either way.
>>
>> Cheers,
>> John Stone
>> [3]vmd_at_ks.uiuc.edu
>>
>> On Thu, Feb 12, 2015 at 05:48:30PM +0100, Michael Patzschke wrote:
>>
>> Hello John,
>>
>> Thank you for your fast reply. My apologies for being a bit vague
>> in my last mail:
>>
>> Both the 2012 and the 2014 Mac run the same MacOS. On the old
>> machine the cube files still load perfectly and everything else works
>> as expected. On the new machine the OpenGL window freezes.
>> This is true for both for 1.9.2. and 1.9.1.
>>
>> The cube files were generated with different codes (i.e. MultiWFN,
>> nciplot and such) none of them works. The new Mac has 16GB of
>> memory and about 6 are free. It uses and Intel Iris Pro card with
>> 1,5 GB dedicated RAM.
>>
>> I have tried everything now and the only thing that does work on the
>> new machine is opening a pdb file over the net. Everything else fails.
>> I have been using Macs for a long time and I feel rather stupid now.
>> I am grateful for any advice???
>>
>> Regards,
>> Michael
>>
>> On 12 Feb 2015, at 17:04, John Stone <[4]johns_at_ks.uiuc.edu> wrote:
>>
>> Michael,
>> It's possibly a MacOS X issue if you have recently upgraded your
>> machines
>> to Yosemite. That said, it's worth asking more details about the
>> cube
>> files also. So, the problem only occurs when loading cube files,
>> but
>> everything else is fine? We haven't changed anything terribly
>> significant
>> in the Gaussian cube file reader recently. Axel taught it to
>> recognize cube
>> files from g09 rev d.01 back in 2013, but that's the only change
>> since 2009.
>> Perhaps your cube files are a particular variant of the format that
>> the
>> VMD plugin doesn't handle yet? What Gaussian rev generated them?
>>
>> Cheers,
>> John Stone
>> [5]vmd_at_ks.uiuc.edu
>>
>> On Thu, Feb 12, 2015 at 04:08:12PM +0100, Michael Patzschke wrote:
>>
>> Hi,
>>
>> This is most probably a Mac issue, but I would appreciate any
>> advice.
>> I have been using VMD for years on my MacBook Air (2012). Now I
>> have
>> a new MacBook Pro (mid 2014) and to my dismay, loading gaussian
>> cube
>> files does not work any more.
>>
>> I can load pdb files and other structural files and manipulate
>> them, but as
>> soon as I start loading cube files, the OpenGL Display window just
>> freezes.
>> This happens with both vmd 1.9.2 and 1.9.1
>>
>> Both Macs have a very similar setup (Quartz and MacPorts installed
>> with quite
>> a number of graphical routine ports installed, but I highly doubt,
>> that they would
>> interfere with vmd)
>>
>> I would very much appreciate any help or hints how to solve this
>> problem!
>>
>> Regards,
>> Michael
>>
>> --
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> [6]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> [7]http://www.ks.uiuc.edu/Research/vmd/
>>
>> --
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> [8]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> [9]http://www.ks.uiuc.edu/Research/vmd/
>>
>> References
>>
>> Visible links
>> 1. http://pdb.org/
>> 2. mailto:johns_at_ks.uiuc.edu
>> 3. mailto:vmd_at_ks.uiuc.edu
>> 4. mailto:johns_at_ks.uiuc.edu
>> 5. mailto:vmd_at_ks.uiuc.edu
>> 6. http://www.ks.uiuc.edu/~johns/
>> 7. http://www.ks.uiuc.edu/Research/vmd/
>> 8. http://www.ks.uiuc.edu/~johns/
>> 9. http://www.ks.uiuc.edu/Research/vmd/
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/